This doesn't answer your question directly, but I wanted to throw a couple things out:
I generally find it counter-productive to separate generated code. I always like to generally follow the "one class per file" rule, but I make an exception here, because I often deal with very large schemas. Even in their own directory, I don't want to have to diff tens (to hundreds) of files when I generate a new version of the code. I find it very convenient to have all the generated code diffable in one file.
Now, to offer a possible solution - Resharper has the ability to pull all the classes out of a file and put them in their own files. If you right click the file in the solution explorer, you can say Refactor → Move types into matching files.... Of course, this isn't anywhere near as convenient as just generating it this way, but I don't know of a tool that will do that.
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